First draft genome assembly of the Argane tree (Argania spinosa)
| Autor: | Slimane Khayi, S. Essayeh, A. Legssyer, M. Ganoudi, Rachid Dahan, M. Memari, Driss Iraqi, Y. Vande Peer, Hassan Ghazal, M. Alaoui Mdarhi, Bouchra Chaouni, M. Gonzalo Claros, Ghizlane Diria, Tatiana Tatusova, Hayat Sedrati, A. El Mousadik, Rabha Abdelwahd, Stacy Pirro, David A. Lightfoot, Rachid Mrabet, M. Khalfaoui, Noureddine Hamamouch, Jamila Mouhaddab, Turgay Unver, Rachid Mentag, Juan de Dios Alché Ramírez, Mustapha Labhilili, Oussama Badad, Noureddine Boukhatem, N. Elhouda Azza, B. Rahim, R. Merrouch, Fatima Gaboun, Mohamed Badraoui |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Engineering Argania spinosa Genome General Immunology and Microbiology business.industry Assembly Biology and Life Sciences Sequence assembly Library science General Medicine General Biochemistry Genetics and Molecular Biology International Argane Genome Consortium Endemic Morocco 03 medical and health sciences Tree (data structure) Argane 030104 developmental biology Work (electrical) General Pharmacology Toxicology and Pharmaceutics business |
| Zdroj: | F1000RESEARCH |
| ISSN: | 2046-1402 |
| Popis: | Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes. |
| Databáze: | OpenAIRE |
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