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Background   Carex  L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of  Carex  is complex and the classification is not clear. In order to investigate the gene function annotation of  Carex , RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79  Carex  germplasms.    Results  In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei’s (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What’s more, the fingerprints of 79  Carex  species are established in this study. Different combinations of primer pairs can be used to identify multiple  Carex  at one time, which overcomes the difficulties of traditional identification methods.    Conclusions  The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79  Carex  species. These markers can be used to investigate the evolutionary history of  Carex  and related species, as well as to serve as a guide in future breeding projects.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02792-8.

The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species