Lactuca super-pangenome provides insights into lettuce genome evolution and domestication
Abstract Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from repre...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62641-w |
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| _version_ | 1849235159809785856 |
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| author | Shuai Cao Nunchanoke Sawettalake Lisha Shen |
| author_facet | Shuai Cao Nunchanoke Sawettalake Lisha Shen |
| author_sort | Shuai Cao |
| collection | DOAJ |
| description | Abstract Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. These assemblies exhibit diverse genome sizes ranging from 2.1 Gb to 5.5 Gb with abundant repetitive sequences, and expansion of repetitive sequences, associated with low DNA methylation levels, likely contributes to the genome size variations. Furthermore, by constructing a graph-based lettuce pangenome reference, we explore the landscape, genomic, and epigenetic features of structural variations, and reveal their contributions to gene expression and domestication. We also identify copy number variations in FLOWERING LOCUS C in association with delayed flowering in cultivated lettuce. Overall, this comprehensive Lactuca super-pangenome assembly will expedite functional genomics studies and breeding efforts of this globally important crop. |
| format | Article |
| id | doaj-art-ab40c87b633f471ba73f5ecf9caa7370 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-ab40c87b633f471ba73f5ecf9caa73702025-08-20T04:02:54ZengNature PortfolioNature Communications2041-17232025-08-0116111410.1038/s41467-025-62641-wLactuca super-pangenome provides insights into lettuce genome evolution and domesticationShuai Cao0Nunchanoke Sawettalake1Lisha Shen2Temasek Life Sciences Laboratory, 1 Research Link, National University of SingaporeTemasek Life Sciences Laboratory, 1 Research Link, National University of SingaporeTemasek Life Sciences Laboratory, 1 Research Link, National University of SingaporeAbstract Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. These assemblies exhibit diverse genome sizes ranging from 2.1 Gb to 5.5 Gb with abundant repetitive sequences, and expansion of repetitive sequences, associated with low DNA methylation levels, likely contributes to the genome size variations. Furthermore, by constructing a graph-based lettuce pangenome reference, we explore the landscape, genomic, and epigenetic features of structural variations, and reveal their contributions to gene expression and domestication. We also identify copy number variations in FLOWERING LOCUS C in association with delayed flowering in cultivated lettuce. Overall, this comprehensive Lactuca super-pangenome assembly will expedite functional genomics studies and breeding efforts of this globally important crop.https://doi.org/10.1038/s41467-025-62641-w |
| spellingShingle | Shuai Cao Nunchanoke Sawettalake Lisha Shen Lactuca super-pangenome provides insights into lettuce genome evolution and domestication Nature Communications |
| title | Lactuca super-pangenome provides insights into lettuce genome evolution and domestication |
| title_full | Lactuca super-pangenome provides insights into lettuce genome evolution and domestication |
| title_fullStr | Lactuca super-pangenome provides insights into lettuce genome evolution and domestication |
| title_full_unstemmed | Lactuca super-pangenome provides insights into lettuce genome evolution and domestication |
| title_short | Lactuca super-pangenome provides insights into lettuce genome evolution and domestication |
| title_sort | lactuca super pangenome provides insights into lettuce genome evolution and domestication |
| url | https://doi.org/10.1038/s41467-025-62641-w |
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