Yunnan 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 University, Kunming, 650224, PR, China.
Technology Center of Kunming Customs, Kunming, 650228, PR, China.
BMC Genomics. 2024 Oct 23;25(1):993. doi: 10.1186/s12864-024-10917-8.
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.
Garuga Roxb. 是一个特有于中国西南和东南亚其他热带地区的属，由于热带森林的丧失和土地利用的变化，该属面临灭绝的风险。对 G. forrestii 进行基因组调查有助于更深入地了解和保护该属。
本研究利用 G. forrestii 的基因组调查产生了约 54.56GB 的序列数据，覆盖率约为 112×。K-mer 分析表明，基因组大小约为 0.48GB，小于流式细胞术估计的 0.52GB。杂合度约为 0.54%，重复率约为 51.54%。所有的鸟枪法数据都组装成 339729 个支架，N50 为 17344bp。鸟嘌呤和胞嘧啶的平均含量约为 35.16%。共检测到 330999 个 SSRs，其中单核苷酸重复最多，占 70.16%，其次是二核苷酸重复，占 20.40%。我们使用 Smudgeplot 进行了初步的倍性评估，在 G. forrestii 中观察到相对覆盖深度和总覆盖深度（2n）的 1/2 处有明显的双峰分布，表明可能存在二倍体基因组结构。使用 G. forrestii 的伪染色体和 Boswellia sacra 的基因组作为参考基因组，在三个 Garuga 物种中进行了引物种群重测序分析。主成分分析（PCA）表明存在三个不同的组，但基于不同参考基因组数据集和母系与核基因组之间的全基因组系统发育分析结果存在冲突。
总之，G. forrestii 的基因组较小，Garuga 属内的系统发育关系较为复杂。本研究提供的遗传数据对于全面的全基因组分析、种群遗传多样性评估、适应性进化研究、人工繁殖的推进以及物种保护和恢复计划的支持具有重要价值。最终，本研究有助于加强自然生态系统的保护和管理，促进生物多样性保护，推进可持续发展。
