Development of genomic resources for Nothofagus species using next‐generation sequencing data
Using next‐generation sequencing, we developed the first whole‐genome resources for two hybridizing Nothofagus species of the Patagonian forests that crucially lack genomic data, despite their ecological and industrial value. A de novo assembly strategy combining base quality control and optimizatio...
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| Format: | info:ar-repo/semantics/artículo |
| Language: | Inglés |
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Wiley
2019
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| Online Access: | https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12276 http://hdl.handle.net/20.500.12123/4930 https://doi.org/10.1111/1755-0998.12276 |
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| author | El Mujtar, Veronica Andrea Gallo, Leonardo Ariel Lang, T. Garnier‐Géré, Pauline |
| author_browse | El Mujtar, Veronica Andrea Gallo, Leonardo Ariel Garnier‐Géré, Pauline Lang, T. |
| author_facet | El Mujtar, Veronica Andrea Gallo, Leonardo Ariel Lang, T. Garnier‐Géré, Pauline |
| author_sort | El Mujtar, Veronica Andrea |
| collection | INTA Digital |
| description | Using next‐generation sequencing, we developed the first whole‐genome resources for two hybridizing Nothofagus species of the Patagonian 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 Nothofagus 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 cpDNA 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. Nothofagus obliqua had more alleles (4.89) on average than N. nervosa (2.89), 8 SSRs were efficient to discriminate species, and three were successfully transferred in three other Nothofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in Nothofagus species, and for conserving and managing natural populations. |
| format | info:ar-repo/semantics/artículo |
| id | INTA4930 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | INTA49302019-04-17T13:16:23Z Development of genomic resources for Nothofagus species using next‐generation sequencing data El Mujtar, Veronica Andrea Gallo, Leonardo Ariel Lang, T. Garnier‐Géré, Pauline Nothofagus Recursos Genéticos Secuencia Nucleotídica Hibridación Genomas Genetic Resources Nucleotide Sequence Hybridization Genomes Nothofagus nervosa Nothofagus obliqua Using next‐generation sequencing, we developed the first whole‐genome resources for two hybridizing Nothofagus species of the Patagonian 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 Nothofagus 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 cpDNA 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. Nothofagus obliqua had more alleles (4.89) on average than N. nervosa (2.89), 8 SSRs were efficient to discriminate species, and three were successfully transferred in three other Nothofagus species. These resources will greatly help for future inferences of demographic, adaptive and hybridizing events in Nothofagus species, and for conserving and managing natural populations. EEA Bariloche Fil: El Mujtar, Veronica Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Unidad de Genética Ecológica y Mejoramiento Forestal; Argentina. Institut National de la Recherche Agronomique. Biodiversity Genes & Communities Biodiversity Genes & Communities; Francia Fil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Unidad de Genética Ecológica y Mejoramiento Forestal; Argentina Fil: Lang, T. Chinese Academy of Sciences. Xishuangbanna Tropical Botanical Garden. Key Laboratory of Tropical Forest Ecology; China Fil: Garnier‐Géré, Pauline. Institut National de la Recherche Agronomique. Biodiversity Genes & Communities Biodiversity Genes & Communities; Francia 2019-04-17T13:14:46Z 2019-04-17T13:14:46Z 2014-11 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12276 http://hdl.handle.net/20.500.12123/4930 1755-098X 1755-0998 https://doi.org/10.1111/1755-0998.12276 eng info:eu-repo/semantics/restrictedAccess application/pdf Wiley Molecular Ecology Resources 14 (6) : 1281-1295 (November 2014) |
| spellingShingle | Nothofagus Recursos Genéticos Secuencia Nucleotídica Hibridación Genomas Genetic Resources Nucleotide Sequence Hybridization Genomes Nothofagus nervosa Nothofagus obliqua El Mujtar, Veronica Andrea Gallo, Leonardo Ariel Lang, T. Garnier‐Géré, Pauline Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title | Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title_full | Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title_fullStr | Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title_full_unstemmed | Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title_short | Development of genomic resources for Nothofagus species using next‐generation sequencing data |
| title_sort | development of genomic resources for nothofagus species using next generation sequencing data |
| topic | Nothofagus Recursos Genéticos Secuencia Nucleotídica Hibridación Genomas Genetic Resources Nucleotide Sequence Hybridization Genomes Nothofagus nervosa Nothofagus obliqua |
| url | https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12276 http://hdl.handle.net/20.500.12123/4930 https://doi.org/10.1111/1755-0998.12276 |
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