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An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecul...
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/PMC5967340/ https://www.ncbi.nlm.nih.gov/pubmed/29795526 http://dx.doi.org/10.1038/s41598-018-26416-2 |
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author | Ruggieri, Valentino Alexiou, Konstantinos G. Morata, Jordi Argyris, Jason Pujol, Marta Yano, Ryoichi Nonaka, Satoko Ezura, Hiroshi Latrasse, David Boualem, Adnane Benhamed, Moussa Bendahmane, Abdelhafid Cigliano, Riccardo Aiese Sanseverino, Walter Puigdomènech, Pere Casacuberta, Josep M. Garcia-Mas, Jordi |
author_facet | Ruggieri, Valentino Alexiou, Konstantinos G. Morata, Jordi Argyris, Jason Pujol, Marta Yano, Ryoichi Nonaka, Satoko Ezura, Hiroshi Latrasse, David Boualem, Adnane Benhamed, Moussa Bendahmane, Abdelhafid Cigliano, Riccardo Aiese Sanseverino, Walter Puigdomènech, Pere Casacuberta, Josep M. Garcia-Mas, Jordi |
author_sort | Ruggieri, Valentino |
collection | PubMed |
description | We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species. |
format | Online Article Text |
id | pubmed-5967340 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-59673402018-05-30 An improved assembly and annotation of the melon (Cucumis melo L.) reference genome Ruggieri, Valentino Alexiou, Konstantinos G. Morata, Jordi Argyris, Jason Pujol, Marta Yano, Ryoichi Nonaka, Satoko Ezura, Hiroshi Latrasse, David Boualem, Adnane Benhamed, Moussa Bendahmane, Abdelhafid Cigliano, Riccardo Aiese Sanseverino, Walter Puigdomènech, Pere Casacuberta, Josep M. Garcia-Mas, Jordi Sci Rep Article We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species. Nature Publishing Group UK 2018-05-24 /pmc/articles/PMC5967340/ /pubmed/29795526 http://dx.doi.org/10.1038/s41598-018-26416-2 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 Ruggieri, Valentino Alexiou, Konstantinos G. Morata, Jordi Argyris, Jason Pujol, Marta Yano, Ryoichi Nonaka, Satoko Ezura, Hiroshi Latrasse, David Boualem, Adnane Benhamed, Moussa Bendahmane, Abdelhafid Cigliano, Riccardo Aiese Sanseverino, Walter Puigdomènech, Pere Casacuberta, Josep M. Garcia-Mas, Jordi An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title | An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title_full | An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title_fullStr | An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title_full_unstemmed | An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title_short | An improved assembly and annotation of the melon (Cucumis melo L.) reference genome |
title_sort | improved assembly and annotation of the melon (cucumis melo l.) reference genome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967340/ https://www.ncbi.nlm.nih.gov/pubmed/29795526 http://dx.doi.org/10.1038/s41598-018-26416-2 |
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