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An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by ass...

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Autores principales: Ong, Ai-Ling, Teh, Chee-Keng, Mayes, Sean, Massawe, Festo, Appleton, David Ross, Kulaveerasingam, Harikrishna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692215/
https://www.ncbi.nlm.nih.gov/pubmed/33152992
http://dx.doi.org/10.3390/plants9111476
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author Ong, Ai-Ling
Teh, Chee-Keng
Mayes, Sean
Massawe, Festo
Appleton, David Ross
Kulaveerasingam, Harikrishna
author_facet Ong, Ai-Ling
Teh, Chee-Keng
Mayes, Sean
Massawe, Festo
Appleton, David Ross
Kulaveerasingam, Harikrishna
author_sort Ong, Ai-Ling
collection PubMed
description Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.
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spelling pubmed-76922152020-11-28 An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily Ong, Ai-Ling Teh, Chee-Keng Mayes, Sean Massawe, Festo Appleton, David Ross Kulaveerasingam, Harikrishna Plants (Basel) Article Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae. MDPI 2020-11-03 /pmc/articles/PMC7692215/ /pubmed/33152992 http://dx.doi.org/10.3390/plants9111476 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ong, Ai-Ling
Teh, Chee-Keng
Mayes, Sean
Massawe, Festo
Appleton, David Ross
Kulaveerasingam, Harikrishna
An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title_full An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title_fullStr An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title_full_unstemmed An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title_short An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily
title_sort improved oil palm genome assembly as a valuable resource for crop improvement and comparative genomics in the arecoideae subfamily
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692215/
https://www.ncbi.nlm.nih.gov/pubmed/33152992
http://dx.doi.org/10.3390/plants9111476
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