Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn
Abstract Natural hybridization in sea buckthorn (Hippophae spp.) is well documented. While the parental species involved in these events have been identified, distinctions between F1 hybrids and later-generation (Fn) hybrids remain insufficiently explored, and their genetic compositions are not yet...
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| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-09923-x |
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| author | Hui Zhang Zhiqi Wang Xue Su Dong Han Lujie Yang Ying Zhang Jing Fang Jingyuan Wang Kun Sun |
| author_facet | Hui Zhang Zhiqi Wang Xue Su Dong Han Lujie Yang Ying Zhang Jing Fang Jingyuan Wang Kun Sun |
| author_sort | Hui Zhang |
| collection | DOAJ |
| description | Abstract Natural hybridization in sea buckthorn (Hippophae spp.) is well documented. While the parental species involved in these events have been identified, distinctions between F1 hybrids and later-generation (Fn) hybrids remain insufficiently explored, and their genetic compositions are not yet fully understood. In this study, we employed transcriptomic data and reference genomes to identify Fn hybrids in two natural hybrid populations, confirming eight individuals—including H. goniocarpa Lian. X. L. Chen et K. Sun and four members of a hybrid swarm from Qinghai, China—as F1 hybrids. These findings support the hypothesis that H. goniocarpa is not a distinct species, but rather an F1 hybrid within the genus. Additionally, we discuss limitations specific to SNP calling from transcriptomic data—such as allele-specific expression and low transcript abundance—which may lead to the misclassification of heterozygous sites as homozygous. Finally, we constructed the first phylogenomic tree of the Hippophae genus using transcriptomic data and performed a comparative analysis of interspecific relationships based on SNP and indel markers derived from the same dataset. |
| format | Article |
| id | doaj-art-8ea5b345a19a4d26af2f17d763f70101 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-8ea5b345a19a4d26af2f17d763f701012025-08-20T03:45:30ZengNature PortfolioScientific Reports2045-23222025-07-0115111310.1038/s41598-025-09923-xReidentification of hybridization events with transcriptomic data and phylogenomic study in SeabuckthornHui Zhang0Zhiqi Wang1Xue Su2Dong Han3Lujie Yang4Ying Zhang5Jing Fang6Jingyuan Wang7Kun Sun8College of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityCollege of Life Sciences, Northwest Normal UniversityAbstract Natural hybridization in sea buckthorn (Hippophae spp.) is well documented. While the parental species involved in these events have been identified, distinctions between F1 hybrids and later-generation (Fn) hybrids remain insufficiently explored, and their genetic compositions are not yet fully understood. In this study, we employed transcriptomic data and reference genomes to identify Fn hybrids in two natural hybrid populations, confirming eight individuals—including H. goniocarpa Lian. X. L. Chen et K. Sun and four members of a hybrid swarm from Qinghai, China—as F1 hybrids. These findings support the hypothesis that H. goniocarpa is not a distinct species, but rather an F1 hybrid within the genus. Additionally, we discuss limitations specific to SNP calling from transcriptomic data—such as allele-specific expression and low transcript abundance—which may lead to the misclassification of heterozygous sites as homozygous. Finally, we constructed the first phylogenomic tree of the Hippophae genus using transcriptomic data and performed a comparative analysis of interspecific relationships based on SNP and indel markers derived from the same dataset.https://doi.org/10.1038/s41598-025-09923-xSea BuckthornTranscriptomeSNP callingF1 hybrid identificationPhylogenomics |
| spellingShingle | Hui Zhang Zhiqi Wang Xue Su Dong Han Lujie Yang Ying Zhang Jing Fang Jingyuan Wang Kun Sun Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn Scientific Reports Sea Buckthorn Transcriptome SNP calling F1 hybrid identification Phylogenomics |
| title | Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn |
| title_full | Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn |
| title_fullStr | Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn |
| title_full_unstemmed | Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn |
| title_short | Reidentification of hybridization events with transcriptomic data and phylogenomic study in Seabuckthorn |
| title_sort | reidentification of hybridization events with transcriptomic data and phylogenomic study in seabuckthorn |
| topic | Sea Buckthorn Transcriptome SNP calling F1 hybrid identification Phylogenomics |
| url | https://doi.org/10.1038/s41598-025-09923-x |
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