Genomic Resources for N. nervosa and N. oblique Generated
May 28, 2014 Email"> PrintText Size
Nothofagus nervosa and Nothofagus obliqua are two closely related species among the six endemic species of the genus Nothofagus occurring in Argentina. Both species have economic and industrial value. However, the genomic data of the two species were crucially lacking.
Researchers from Argentina, France, and China used next generation sequencing to develop the first whole genome resources of the two hybridizing Nothofagus species of the Patagonian forests. Dr. LANG Tiange of Xishuangbanna Tropical Botanical Garden (XTBG) participated in the study. The aim of their work was to generate genomic resources for N. nervosa and N. obliqua in order to aid the study of demographic, adaptive and hybridization processes in their natural range.
The researchers used total DNA 1) to complement the available transcriptome resources by obtaining both organelle and nuclear genomic data, 2) to get both non-coding or non-genic sequences that would potentially be less affected by selection, and coding sequences that could be a preferred source of candidate genes for adaptive traits, and 3) to develop SSR and SNP markers for future studies. They reported in particular the full gene map of the Nothofagus chloroplast genome and identification of 52 mitochondrial genes including protein, rRNA and tRNA genes. They also identified 2,274 potential SSRs, 769 of which allowed primer design and were available to validation and transferability to other Nothofagus species. They validated 9 of them, showed that 8 efficiently discriminated both species, and transferred 3 of them to other Nothofagus species (N. antarctica, N. dombeyi and N. pumilio). Finally, they identified quality SNPs that allowed preliminary estimates of diversity among organelle and nuclear genomes and divergence among species.
The study entitled “Development of genomic resources for Nothofagusspecies using next-generation sequencing data” has been published online in Molecular Ecology Resources.
Nothofagus nervosa and Nothofagus obliqua are two closely related species among the six endemic species of the genus Nothofagus occurring in Argentina. Both species have economic and industrial value. However, the genomic data of the two species were crucially lacking.
Researchers from Argentina, France, and China used next generation sequencing to develop the first whole genome resources of the two hybridizing Nothofagus species of the Patagonian forests. Dr. LANG Tiange of Xishuangbanna Tropical Botanical Garden (XTBG) participated in the study. The aim of their work was to generate genomic resources for N. nervosa and N. obliqua in order to aid the study of demographic, adaptive and hybridization processes in their natural range.
The researchers used total DNA 1) to complement the available transcriptome resources by obtaining both organelle and nuclear genomic data, 2) to get both non-coding or non-genic sequences that would potentially be less affected by selection, and coding sequences that could be a preferred source of candidate genes for adaptive traits, and 3) to develop SSR and SNP markers for future studies. They reported in particular the full gene map of the Nothofagus chloroplast genome and identification of 52 mitochondrial genes including protein, rRNA and tRNA genes. They also identified 2,274 potential SSRs, 769 of which allowed primer design and were available to validation and transferability to other Nothofagus species. They validated 9 of them, showed that 8 efficiently discriminated both species, and transferred 3 of them to other Nothofagus species (N. antarctica, N. dombeyi and N. pumilio). Finally, they identified quality SNPs that allowed preliminary estimates of diversity among organelle and nuclear genomes and divergence among species.
The study entitled “Development of genomic resources for Nothofagusspecies using next-generation sequencing data” has been published online in Molecular Ecology Resources.
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