Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour.
Abstract Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicin...
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Nature Portfolio
2024-02-01
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| Online Access: | https://doi.org/10.1038/s41598-024-55498-4 |
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| author | Jianjian Huang Jie Chen Min Shi Jiaqi Zheng Ming Chen Linjun Wu Hui Zhu Yuzhong Zheng Qinghan Wu Fengnian Wu |
| author_facet | Jianjian Huang Jie Chen Min Shi Jiaqi Zheng Ming Chen Linjun Wu Hui Zhu Yuzhong Zheng Qinghan Wu Fengnian Wu |
| author_sort | Jianjian Huang |
| collection | DOAJ |
| description | Abstract Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat–retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family. |
| first_indexed | 2024-03-07T15:03:27Z |
| format | Article |
| id | doaj.art-89cb086a22c94b8289c1a0933ac2369f |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:03:27Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-89cb086a22c94b8289c1a0933ac2369f2024-03-05T19:01:43ZengNature PortfolioScientific Reports2045-23222024-02-0114111110.1038/s41598-024-55498-4Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour.Jianjian Huang0Jie Chen1Min Shi2Jiaqi Zheng3Ming Chen4Linjun Wu5Hui Zhu6Yuzhong Zheng7Qinghan Wu8Fengnian Wu9School of Life Sciences and Food Engineering, Hanshan Normal UniversityCollege of Coastal Agricultural Sciences, Guangdong Ocean UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversitySchool of Life Sciences and Food Engineering, Hanshan Normal UniversityAbstract Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat–retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.https://doi.org/10.1038/s41598-024-55498-4Baccaurea ramifloraWhole-genome sequencingde novo assemblyGenome evolution |
| spellingShingle | Jianjian Huang Jie Chen Min Shi Jiaqi Zheng Ming Chen Linjun Wu Hui Zhu Yuzhong Zheng Qinghan Wu Fengnian Wu Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. Scientific Reports Baccaurea ramiflora Whole-genome sequencing de novo assembly Genome evolution |
| title | Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. |
| title_full | Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. |
| title_fullStr | Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. |
| title_full_unstemmed | Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. |
| title_short | Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. |
| title_sort | genome assembly provides insights into the genome evolution of baccaurea ramiflora lour |
| topic | Baccaurea ramiflora Whole-genome sequencing de novo assembly Genome evolution |
| url | https://doi.org/10.1038/s41598-024-55498-4 |
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