A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species
Abstract Background Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation...
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BMC
2024-10-01
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| Online Access: | https://doi.org/10.1186/s12864-024-10917-8 |
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| author | Dongbo Zhu Rui Rao Yu Du Chunmin Mao Rong Chen Liangliang Yue |
| author_facet | Dongbo Zhu Rui Rao Yu Du Chunmin Mao Rong Chen Liangliang Yue |
| author_sort | Dongbo Zhu |
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| description | Abstract Background Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation of the genus. Results This study utilized genome survey of G. forrestii generated approximately 54.56 GB of sequence data, with approximately 112 × coverage. K-mer analysis indicated a genome size of approximately 0.48 GB, smaller than 0.52GB estimated by flow cytometry. The heterozygosity is of about 0.54%, and a repeat rate of around 51.54%. All the shotgun data were assembled into 339,729 scaffolds, with an N50 of 17,344 bp. The average content of guanine and cytosine was approximately 35.16%. A total of 330,999 SSRs were detected, with mononucleotide repeats being the most abundant at 70.16%, followed by dinucleotide repeats at 20.40%. We conducted a preliminary ploidy assessment using Smudgeplot and observed a clear bimodal distribution in G. forrestii at 1/2 relative coverage depth and total coverage depth (2n), suggesting a potential diploid genome structure. A pseudo chromosome of G. forrestii and a gemone of Boswellia sacra were used as reference genome to perform a primer population resequencing analysis within three Garuga species. Principal component analysis (PCA) indicated three distinct groups, but genome wide phylogenetics represented conflicting both between the dataset of different reference genomes and between maternal and nuclear genome. Conclusion In summary, the genome of G. forrestii is small, and the phylogenetic relationships within the Garuga genus are complex. The genetic data presented in this study holds significant value for comprehensive whole-genome analyses, the evaluation of population genetic diversity, investigations into adaptive evolution, the advancement of artificial breeding efforts, and the support of species conservation and restoration initiatives. Ultimately, this research contributes to reinforcing the conservation and management of natural ecosystems, promoting biodiversity conservation, and advancing sustainable development. |
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| spelling | doaj-art-dc4a04b42b8a479696749bfdee76a6502025-08-20T02:11:24ZengBMCBMC Genomics1471-21642024-10-0125111310.1186/s12864-024-10917-8A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. speciesDongbo Zhu0Rui Rao1Yu Du2Chunmin Mao3Rong Chen4Liangliang Yue5Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, National Plateau Wetlands Research Center, Dianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Southwest Forestry UniversityYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, National Plateau Wetlands Research Center, Dianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Southwest Forestry UniversityTechnology Center of Kunming CustomsYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, National Plateau Wetlands Research Center, Dianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Southwest Forestry UniversityYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, National Plateau Wetlands Research Center, Dianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Southwest Forestry UniversityYunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, National Plateau Wetlands Research Center, Dianchi Lake Ecosystem Observation and Research Station of Yunnan Province, Southwest Forestry UniversityAbstract Background Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation of the genus. Results This study utilized genome survey of G. forrestii generated approximately 54.56 GB of sequence data, with approximately 112 × coverage. K-mer analysis indicated a genome size of approximately 0.48 GB, smaller than 0.52GB estimated by flow cytometry. The heterozygosity is of about 0.54%, and a repeat rate of around 51.54%. All the shotgun data were assembled into 339,729 scaffolds, with an N50 of 17,344 bp. The average content of guanine and cytosine was approximately 35.16%. A total of 330,999 SSRs were detected, with mononucleotide repeats being the most abundant at 70.16%, followed by dinucleotide repeats at 20.40%. We conducted a preliminary ploidy assessment using Smudgeplot and observed a clear bimodal distribution in G. forrestii at 1/2 relative coverage depth and total coverage depth (2n), suggesting a potential diploid genome structure. A pseudo chromosome of G. forrestii and a gemone of Boswellia sacra were used as reference genome to perform a primer population resequencing analysis within three Garuga species. Principal component analysis (PCA) indicated three distinct groups, but genome wide phylogenetics represented conflicting both between the dataset of different reference genomes and between maternal and nuclear genome. Conclusion In summary, the genome of G. forrestii is small, and the phylogenetic relationships within the Garuga genus are complex. The genetic data presented in this study holds significant value for comprehensive whole-genome analyses, the evaluation of population genetic diversity, investigations into adaptive evolution, the advancement of artificial breeding efforts, and the support of species conservation and restoration initiatives. Ultimately, this research contributes to reinforcing the conservation and management of natural ecosystems, promoting biodiversity conservation, and advancing sustainable development.https://doi.org/10.1186/s12864-024-10917-8Genome surveyK-merFlow cytometrySNPPhylogeneticGaruga forrestii |
| spellingShingle | Dongbo Zhu Rui Rao Yu Du Chunmin Mao Rong Chen Liangliang Yue A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species BMC Genomics Genome survey K-mer Flow cytometry SNP Phylogenetic Garuga forrestii |
| title | A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species |
| title_full | A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species |
| title_fullStr | A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species |
| title_full_unstemmed | A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species |
| title_short | A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species |
| title_sort | tip of the iceberg genome survey indicated a complex evolutionary history of garuga roxb species |
| topic | Genome survey K-mer Flow cytometry SNP Phylogenetic Garuga forrestii |
| url | https://doi.org/10.1186/s12864-024-10917-8 |
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