The genome sequence is known for a limited number of plant species including Arabidopsis thaliana, Oryza sativa, Vitis vinifera and Populus trichocarpa. loxophleba, which is, to the best of our knowledge, the highest frequency of SNPs described in woody plant species. In contrast, the more distantly related species contained more SNPs: one in every 16 bp for E. With numerous individuals sampled over the geographical range of each species, we discovered one SNP in every 33 bp for E. Conclusionīy using conservative statistical detection methods, we were confident about the validity of each SNP. The four species share between 20 and 43% of the SNPs in these genes. Neither the pathway nor the position in the pathway influenced gene diversity. loxophleba had much higher SNP diversity. These species also had similar levels of SNP diversity, whereas E. nitens) had similar numbers of SNPs at synonymous and non-synonymous sites. The exons of the two closely related species ( E. We sequenced 23 genes from 1,764 individuals and discovered 8,631 SNPs across the species, with about 1.5 times as many SNPs per kbp in the introns compared to exons. An average sequencing depth of 315 reads per nucleotide site was achieved for all four eucalypt species, Eucalyptus globulus, E. In a single GS-FLX run, we sequenced over 103 Mbp and assembled them to approximately 50 kbp of reference sequences. With this approach the occurrence and patterns of SNP variation for a set of genes can be compared across different species from the same genus. The combination of re-sequencing technologies, large-scale DNA pools and availability of reference gene sequences allowed the extensive characterisation of single nucleotide polymorphisms (SNPs) in genes of four biosynthetic pathways leading to the formation of ecologically relevant secondary metabolites in Eucalyptus. There is little information about the DNA sequence variation within and between closely related plant species.
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