Full-length transcriptome analysis and microsatellite marker development in Euonymus japonicus ‘Beihaidao’

Abstract

Abstract Background Euonymus plants have strong stress resistance and a rich variety of types, making them high-quality garden plant resources for enriching winter greenery and seasonal landscapes in the cold regions of northern China. At present, research on this genus still faces several challenges, such as confusion in germplasm identification and insufficient promotion and application of germplasm resources. In particular, basic research in genomics and genetics remain limited. The overall research on genetic diversity within the genus lags behind, and a systematic germplasm evaluation and breeding system has not yet been formed. Results In this study, Euonymus japonicus ‘Beihaidao’, a cold-resistant evergreen boxwood, was used as the material, and the full-length transcriptome was sequenced and analyzed using single molecule real-time sequencing technology. A batch of polymorphic expressed sequence tag (EST)–simple sequence repeat (SSR) molecular markers was developed, which could provide valuable molecular tools and a data foundation for subsequent genetic diversity analysis, germplasm resource evaluation, and targeted breeding of Euonymus genus germplasm. A total of 280,041 circular consensus reads were obtained via full-length transcriptome sequencing of E. japonicus ‘Beihaidao’, of which 223,742 were full-length non-chimeric sequences. Through clustering and polishing, 88,734 high-quality consensus isoforms were obtained. De-redundancy analysis of the high-quality consensus isoforms yielded 50,741 non-redundant transcript sequences. A total of 78,528 isoforms were successfully annotated in the high-quality isoforms, covering 88.50% of all high-quality isoforms in E. japonicus ‘Beihaidao’. SSR analysis was performed on the non-redundant transcript sequences obtained from the full-length transcriptome, and 36,941 SSR loci were identified with 7 SSR types, mainly single-base repeats (51.56%). Among the 200 designed EST-SSRs, 16 EST-SSR marker pairs with clear amplification bands, good polymorphism, and stable amplification were selected, which used for clustering results in 22 Euonymus germplasm samples. These 16 EST-SSR markers developed from E. japonicus ‘Beihaidao’ transcriptome exhibited stable amplification in both intraspecific accessions and congeneric species, demonstrating excellent intraspecific effectiveness and genus-level interspecific transferability. Conclusions These full-length transcriptome sequencing data and EST-SSR molecular markers provide support for gene discovery and functional genomics research in Euonymus and technical support for molecular-assisted breeding, genetic diversity, and conservation biology research, accelerating the breeding of superior varieties.

The authors' abstract, as published at the source. BMC Plant Biology, 2026 · DOI ↗