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Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo a...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173730/ https://www.ncbi.nlm.nih.gov/pubmed/30320230 http://dx.doi.org/10.1038/s42003-018-0171-y |
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author | Reuscher, Stefan Furuta, Tomoyuki Bessho-Uehara, Kanako Cosi, Michele Jena, Kshirod K. Toyoda, Atsushi Fujiyama, Asao Kurata, Nori Ashikari, Motoyuki |
author_facet | Reuscher, Stefan Furuta, Tomoyuki Bessho-Uehara, Kanako Cosi, Michele Jena, Kshirod K. Toyoda, Atsushi Fujiyama, Asao Kurata, Nori Ashikari, Motoyuki |
author_sort | Reuscher, Stefan |
collection | PubMed |
description | The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species. |
format | Online Article Text |
id | pubmed-6173730 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-61737302018-10-12 Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species Reuscher, Stefan Furuta, Tomoyuki Bessho-Uehara, Kanako Cosi, Michele Jena, Kshirod K. Toyoda, Atsushi Fujiyama, Asao Kurata, Nori Ashikari, Motoyuki Commun Biol Article The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species. Nature Publishing Group UK 2018-10-05 /pmc/articles/PMC6173730/ /pubmed/30320230 http://dx.doi.org/10.1038/s42003-018-0171-y Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Reuscher, Stefan Furuta, Tomoyuki Bessho-Uehara, Kanako Cosi, Michele Jena, Kshirod K. Toyoda, Atsushi Fujiyama, Asao Kurata, Nori Ashikari, Motoyuki Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title | Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title_full | Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title_fullStr | Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title_full_unstemmed | Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title_short | Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species |
title_sort | assembling the genome of the african wild rice oryza longistaminata by exploiting synteny in closely related oryza species |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173730/ https://www.ncbi.nlm.nih.gov/pubmed/30320230 http://dx.doi.org/10.1038/s42003-018-0171-y |
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