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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| Format: | Article |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.868540/full |
| _version_ | 1798036141552697344 |
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| author | Tao Wu Ting Ma Tian Xu Li Pan Yanli Zhang Yongjie Li Delu Ning |
| author_facet | Tao Wu Ting Ma Tian Xu Li Pan Yanli Zhang Yongjie Li Delu Ning |
| author_sort | Tao Wu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-11T21:08:25Z |
| format | Article |
| id | doaj.art-fa0fc2431a3f470983f254dc5928b561 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T21:08:25Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-fa0fc2431a3f470983f254dc5928b5612022-12-22T04:03:09ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-08-011310.3389/fgene.2022.868540868540The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close RelativeTao WuTing MaTian XuLi PanYanli ZhangYongjie LiDelu NingThe 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.https://www.frontiersin.org/articles/10.3389/fgene.2022.868540/fullOlea europaea subsp. cuspidateolive subspecieswild olivegenomeHi-C |
| spellingShingle | Tao Wu Ting Ma Tian Xu Li Pan Yanli Zhang Yongjie Li Delu Ning The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative Frontiers in Genetics Olea europaea subsp. cuspidate olive subspecies wild olive genome Hi-C |
| 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 | Olea europaea subsp. cuspidate olive subspecies wild olive genome Hi-C |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.868540/full |
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