A tip of the iceberg: genome survey indicated a complex evolutionary history of Garuga Roxb. species

• Published in: BMC genomics 2024-10, Vol.25 (1), p.993-13, Article 993
• Main Authors: Zhu, Dongbo, Rao, Rui, Du, Yu, Mao, Chunmin, Chen, Rong, Yue, Liangliang
• Format: Article
• Language: English
• Subjects: Biodiversity; Biological diversity; Biological diversity conservation; Breeding; Conservation; Conserved sequence; Cytosine; Deciduous trees; Diploids; Diseases and pests; Ecosystem management; Endangered & extinct species; Endemic species; Environmental aspects; Evolution, Molecular; Evolutionary biology; Evolutionary conservation; Evolutionary genetics; Extinction (Biology); Flow cytometry; Garuga forrestii; Genetic analysis; Genetic aspects; Genetic diversity; Genetic testing; Genome Size; Genome survey; Genome, Plant; Genomes; Genomic analysis; Genomics; Genomics - methods; Geographical distribution; Growth; Heterozygosity; K-mer; Land conservation; Land use; Leaves; Methods; Microsatellite Repeats; Nucleotide sequence; Phylogenetic; Phylogeny; Ploidy; Population genetics; Population studies; Principal components analysis; Protection and preservation; R&D; Research & development; Rivers; SNP; Software; Species extinction; Surveys; Sustainable development; Taxonomy; Tropical environment; Tropical environments; Tropical forests; Wildlife conservation
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10917-8

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.