Development of genomic resources for N othofagus species using next‐generation sequencing data

Using next‐generation sequencing, we developed the first whole‐genome resources for two hybridizing N othofagus species of the P atagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimization of the putative chloroplast gene map yielded ~32 000 contigs from 43% of the reads produced. With 12.5% of assembled reads, we covered ~96% of the chloroplast genome and ~70% of the mitochondrial gene content, providing functional and structural annotations for 112 and 52 genes, respectively. Functional annotation was possible on 15% of the contigs, with ~1750 potentially novel nuclear genes identified for N othofagus species. We estimated that the new resources (13.41 Mb in total) included ~4000 gene regions representing ~6.5% of the expected genic partition of the genome, the remaining contigs potentially being nongenic DNA . A high‐quality single nucleotide polymorphisms resource was developed by comparing various filtering methods, and preliminary results indicate a strong conservation of cp DNA genomes in contrast to numerous exclusive nuclear polymorphisms in both species. Finally, we characterized 2274 potential simple sequence repeat ( SSR ) loci, designed primers for 769 of them and validated nine of 29 loci in 42 individuals per species. N othofagus obliqua had more alleles (4.89) on average than N . nervosa (2.89), 8 SSR s were efficient to discriminate species, and three were successfully transferred in three other N othofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in N othofagus species, and for conserving and managing natural populations.