The whole-genome survey of Acer griseum, its polymorphic simple sequence repeats development and application

Abstract

Background: Acer griseum Pax is an endangered species endemic to China with both ornamental and economic value. However, the lack of information on its genome size and characteristics hinders further work at the genome level. Methods: This paper applied bioinformatics methods to predict the characteristics and patterns of the A. griseum genome, providing an important basis for formulating its whole-genome sequencing scheme. This study also characterized the simple sequence repeats (SSRs) of A. griseum, laying the foundation for the development and application of genome-wide SSR markers. In this study, PE150 sequencing was performed by the BGI MGISEQ platform, and the sequence files were analyzed by the K-mer method to estimate the characteristic information by GCE software. Results: The genome size was finally determined to be 739.63 Mb, its heterozygosity ratio was 1.33%, and the repetition ratio was 65.68%. A total of 825,960 SSR loci were identified in the assembled genome sequence, and primers were successfully designed for 526,020 loci. To verify the effectiveness of these primers, 100 pairs of primers were randomly selected and synthesized, and 81 pairs successfully amplified the target fragments. Fourteen pairs of primers with good polymorphism were selected for principal component analysis of 31 A. griseum individuals from two populations, showing favorable heterozygosity and PIC values. According to the findings, these SSRs might identify genetic variations based on geographic areas. Conclusion: It is suggested that Illumina + PacBio assembly strategy should be used for whole-genome sequencing due to the high heterozygosity rate and high repetition rate of the genome. In addition, the SSR primers designed in batches in this study laid a foundation for the in-depth study of population structure and population maintenance mechanism of A. griseum, which is helpful for the effective conservation and sustainable utilization of this germplasm resource.