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The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative

The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our underst...

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Autores principales: Wu, Tao, Ma, Ting, Xu, Tian, Pan, Li, Zhang, Yanli, Li, Yongjie, Ning, Delu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9454953/
https://www.ncbi.nlm.nih.gov/pubmed/36092936
http://dx.doi.org/10.3389/fgene.2022.868540
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author Wu, Tao
Ma, Ting
Xu, Tian
Pan, Li
Zhang, Yanli
Li, Yongjie
Ning, Delu
author_facet Wu, Tao
Ma, Ting
Xu, Tian
Pan, Li
Zhang, Yanli
Li, Yongjie
Ning, Delu
author_sort Wu, Tao
collection PubMed
description The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding of the evolution of this species. Using a hybrid approach by incorporating Illumina, MGI, Nanopore, and Hi-C technologies, we obtained a 1.20-Gb genome assembly for the olive subspecies, Olea europaea subsp. cuspidate (OC), with contig and scaffold N50 values of 5.33 and 50.46 Mb, respectively. A total of 43,511 protein-coding genes were predicted from the genome. Interestingly, we observed a large region (37.5 Mb) of “gene-desert” also called “LTR-hotspot” on chromosome 17. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.39 Mya (95% CI: 2.58–6.23 Mya). The pathways of positively selected genes of OC are related to the metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further research and utilization. In summary, we constructed the de novo genome assembly and protein-coding gene pool for Olea europaea subsp. cuspidate (OC) in this study, which may facilitate breeding applications of improved olive varieties from this widely distributed olive close relative.
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spelling pubmed-94549532022-09-09 The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative Wu, Tao Ma, Ting Xu, Tian Pan, Li Zhang, Yanli Li, Yongjie Ning, Delu Front Genet Genetics The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding of the evolution of this species. Using a hybrid approach by incorporating Illumina, MGI, Nanopore, and Hi-C technologies, we obtained a 1.20-Gb genome assembly for the olive subspecies, Olea europaea subsp. cuspidate (OC), with contig and scaffold N50 values of 5.33 and 50.46 Mb, respectively. A total of 43,511 protein-coding genes were predicted from the genome. Interestingly, we observed a large region (37.5 Mb) of “gene-desert” also called “LTR-hotspot” on chromosome 17. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.39 Mya (95% CI: 2.58–6.23 Mya). The pathways of positively selected genes of OC are related to the metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further research and utilization. In summary, we constructed the de novo genome assembly and protein-coding gene pool for Olea europaea subsp. cuspidate (OC) in this study, which may facilitate breeding applications of improved olive varieties from this widely distributed olive close relative. Frontiers Media S.A. 2022-08-25 /pmc/articles/PMC9454953/ /pubmed/36092936 http://dx.doi.org/10.3389/fgene.2022.868540 Text en Copyright © 2022 Wu, Ma, Xu, Pan, Zhang, Li and Ning. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Wu, Tao
Ma, Ting
Xu, Tian
Pan, Li
Zhang, Yanli
Li, Yongjie
Ning, Delu
The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title_full The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title_fullStr The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title_full_unstemmed The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title_short The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative
title_sort de novo genome assembly of olea europaea subsp. cuspidate, a widely distributed olive close relative
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9454953/
https://www.ncbi.nlm.nih.gov/pubmed/36092936
http://dx.doi.org/10.3389/fgene.2022.868540
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